Her family gathered at her Scottish estate after concerns grew about her health earlier on Thursday.
The Queen came to the throne in 1952 and witnessed enormous social change.
With her death, her eldest son Charles, the former Prince of Wales, will lead the country in mourning as the new King and head of state for 14 Commonwealth realms.
In a statement, Buckingham Palace said: “The Queen died peacefully at Balmoral this afternoon.
“The King and the Queen Consort will remain at Balmoral this evening and will return to London tomorrow.”
All the Queen’s children travelled to Balmoral, near Aberdeen, after doctors placed the Queen under medical supervision.
Her grandson, Prince William, is also there, with his brother, Prince Harry, on his way.
Queen Elizabeth II’s tenure as head of state spanned post-war austerity, the transition from empire to Commonwealth, the end of the Cold War and the UK’s entry into – and withdrawal from – the European Union.
Her reign spanned 15 prime ministers starting with Winston Churchill, born in 1874, and including Liz Truss, born 101 years later in 1975, and appointed by the Queen earlier this week.
She held weekly audiences with her prime minister throughout her reign.
The Queen was born Elizabeth Alexandra Mary Windsor, in Mayfair, London, on 21 April 1926.